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Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations

BACKGROUND: Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host’s gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However,...

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Autores principales: Umu, Özgün C O, Frank, Jeremy A, Fangel, Jonatan U, Oostindjer, Marije, da Silva, Carol Souza, Bolhuis, Elizabeth J, Bosch, Guido, Willats, William G T, Pope, Phillip B, Diep, Dzung B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405844/
https://www.ncbi.nlm.nih.gov/pubmed/25905018
http://dx.doi.org/10.1186/s40168-015-0078-5
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author Umu, Özgün C O
Frank, Jeremy A
Fangel, Jonatan U
Oostindjer, Marije
da Silva, Carol Souza
Bolhuis, Elizabeth J
Bosch, Guido
Willats, William G T
Pope, Phillip B
Diep, Dzung B
author_facet Umu, Özgün C O
Frank, Jeremy A
Fangel, Jonatan U
Oostindjer, Marije
da Silva, Carol Souza
Bolhuis, Elizabeth J
Bosch, Guido
Willats, William G T
Pope, Phillip B
Diep, Dzung B
author_sort Umu, Özgün C O
collection PubMed
description BACKGROUND: Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host’s gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However, few studies have focused on how they influence the gut microbiome and how these interactions influence host health. The aim of this study is to investigate how the gut microbiome of growing pigs responds to diets containing gel-forming alginate and fermentable resistant starch and to predict important interactions and functional changes within the microbiota. RESULTS: Nine growing pigs (3-month-old), divided into three groups, were fed with either a control, alginate-, or resistant starch-containing diet (CON, ALG, or RS), and fecal samples were collected over a 12-week period. SSU (small subunit) rDNA amplicon sequencing data was annotated to assess the gut microbiome, whereas comprehensive microarray polymer profiling (CoMPP) of digested material was employed to evaluate feed degradation. Gut microbiome structure variation was greatest in pigs fed with resistant starch, where notable changes included the decrease in alpha diversity and increase in relative abundance of Lachnospiraceae- and Ruminococcus-affiliated phylotypes. Imputed function was predicted to vary significantly in pigs fed with resistant starch and to a much lesser extent with alginate; however, the key pathways involving degradation of starch and other plant polysaccharides were predicted to be unaffected. The change in relative abundance levels of basal dietary components (plant cell wall polysaccharides and proteins) over time was also consistent irrespective of diet; however, correlations between the dietary components and phylotypes varied considerably in the different diets. CONCLUSIONS: Resistant starch-containing diet exhibited the strongest structural variation compared to the alginate-containing diet. This variation gave rise to a microbiome that contains phylotypes affiliated with metabolically reputable taxonomic lineages. Despite the significant microbiome structural shifts that occurred from resistant starch-containing diet, functional redundancy is seemingly apparent with respect to the microbiome’s capacity to degrade starch and other dietary polysaccharides, one of the key stages in digestion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0078-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-44058442015-04-23 Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations Umu, Özgün C O Frank, Jeremy A Fangel, Jonatan U Oostindjer, Marije da Silva, Carol Souza Bolhuis, Elizabeth J Bosch, Guido Willats, William G T Pope, Phillip B Diep, Dzung B Microbiome Research BACKGROUND: Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host’s gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However, few studies have focused on how they influence the gut microbiome and how these interactions influence host health. The aim of this study is to investigate how the gut microbiome of growing pigs responds to diets containing gel-forming alginate and fermentable resistant starch and to predict important interactions and functional changes within the microbiota. RESULTS: Nine growing pigs (3-month-old), divided into three groups, were fed with either a control, alginate-, or resistant starch-containing diet (CON, ALG, or RS), and fecal samples were collected over a 12-week period. SSU (small subunit) rDNA amplicon sequencing data was annotated to assess the gut microbiome, whereas comprehensive microarray polymer profiling (CoMPP) of digested material was employed to evaluate feed degradation. Gut microbiome structure variation was greatest in pigs fed with resistant starch, where notable changes included the decrease in alpha diversity and increase in relative abundance of Lachnospiraceae- and Ruminococcus-affiliated phylotypes. Imputed function was predicted to vary significantly in pigs fed with resistant starch and to a much lesser extent with alginate; however, the key pathways involving degradation of starch and other plant polysaccharides were predicted to be unaffected. The change in relative abundance levels of basal dietary components (plant cell wall polysaccharides and proteins) over time was also consistent irrespective of diet; however, correlations between the dietary components and phylotypes varied considerably in the different diets. CONCLUSIONS: Resistant starch-containing diet exhibited the strongest structural variation compared to the alginate-containing diet. This variation gave rise to a microbiome that contains phylotypes affiliated with metabolically reputable taxonomic lineages. Despite the significant microbiome structural shifts that occurred from resistant starch-containing diet, functional redundancy is seemingly apparent with respect to the microbiome’s capacity to degrade starch and other dietary polysaccharides, one of the key stages in digestion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0078-5) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-16 /pmc/articles/PMC4405844/ /pubmed/25905018 http://dx.doi.org/10.1186/s40168-015-0078-5 Text en © Umu et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Umu, Özgün C O
Frank, Jeremy A
Fangel, Jonatan U
Oostindjer, Marije
da Silva, Carol Souza
Bolhuis, Elizabeth J
Bosch, Guido
Willats, William G T
Pope, Phillip B
Diep, Dzung B
Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title_full Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title_fullStr Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title_full_unstemmed Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title_short Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
title_sort resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405844/
https://www.ncbi.nlm.nih.gov/pubmed/25905018
http://dx.doi.org/10.1186/s40168-015-0078-5
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